Contacts of the helix formed by residues 397 - 419 (chain A) in PDB entry 3EIJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PRO 4.7 3.1 + - - -
360A HIS* 5.1 0.7 + - - -
391A TRP* 3.9 1.8 - - - -
394A SER* 4.9 9.9 - - - +
395A THR 3.7 4.3 + - - +
396A ILE* 1.3 79.3 - - - +
398A VAL* 1.3 68.9 + - + +
399A ASP* 4.3 6.4 + - - +
400A GLN* 3.9 21.6 + - - +
401A MET* 3.1 19.1 + - - +
212B LYS* 3.4 29.6 - - - +
214B SER* 5.0 12.3 - - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TRP* 3.6 29.2 - - + -
397A THR* 1.3 72.6 - - - +
399A ASP* 1.3 55.9 + - - +
401A MET* 3.5 2.7 - - + +
402A LYS* 2.6 43.8 + - + +
443A LEU* 6.2 2.2 - - + -
176B PHE 3.7 16.4 - - - +
177B GLU* 3.1 24.7 - - - +
178B HIS 3.5 28.5 - - - +
179B GLY* 4.2 3.4 - - - +
218B MET* 4.5 8.7 - - + -
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A THR* 3.4 5.5 - - - +
398A VAL* 1.3 78.5 - - - +
400A GLN* 1.3 64.7 + - - +
402A LYS* 3.0 7.8 + - - +
403A ARG* 2.6 39.7 + - - +
214B SER* 3.9 18.0 - - - +
217B GLU* 3.3 30.3 - - - +
218B MET* 4.3 24.0 - - + -
221B LYS* 3.4 21.3 + - - -
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PRO 3.1 21.1 - - - +
358A HIS* 3.2 30.4 + - - +
360A HIS* 3.3 17.6 + - + +
361A HIS* 2.8 62.9 + - - +
396A ILE* 4.0 4.0 - - + -
397A THR* 3.6 18.8 + - - +
399A ASP* 1.3 92.2 + - - +
401A MET* 1.3 63.2 + - - +
403A ARG* 4.4 1.8 - - - +
404A GLY* 3.1 18.9 + - - -
214B SER* 6.1 1.4 - - - -
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Residues in contact with MET 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 4.0 12.5 - - - +
387A LEU* 4.6 17.5 - - + +
391A TRP* 4.6 9.6 - - + -
396A ILE* 3.5 22.3 - - + +
397A THR 3.1 18.7 + - - +
398A VAL* 3.6 7.0 - - + +
400A GLN* 1.3 77.0 - - - +
402A LYS* 1.3 61.9 + - - +
404A GLY* 3.5 1.6 + - - -
405A TYR* 2.8 58.7 + - + +
438A ILE* 3.3 56.3 - - + +
439A ILE* 4.0 4.9 - - + -
443A LEU* 5.1 1.1 - - + -
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 2.6 26.0 + - + +
399A ASP* 3.5 7.6 - - - +
401A MET* 1.3 72.2 - - - +
403A ARG* 1.3 65.8 + - - +
405A TYR* 3.3 4.2 + - - +
406A GLU* 3.1 45.2 + - - +
442A GLN* 4.2 10.2 + - - +
443A LEU* 3.5 31.5 - - + +
175B TYR* 4.7 6.3 + - - -
179B GLY* 3.1 33.8 + - - +
181B THR* 5.0 4.0 + - - -
218B MET* 5.9 4.5 - - - +
221B LYS* 3.8 33.9 - - - +
225B ASP* 5.7 1.2 + - - -
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 3.5 38.0 + - + +
399A ASP* 2.6 26.9 + - - +
400A GLN* 4.4 2.2 - - - +
402A LYS* 1.3 75.3 - - - +
404A GLY* 1.3 61.5 + - - +
406A GLU* 3.3 14.5 + - - +
407A ARG* 3.1 48.7 + - - +
221B LYS* 5.0 11.0 - - - +
326B HIS* 3.7 27.1 + - - +
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 3.7 23.3 - - - +
364A VAL* 3.9 18.6 - - - -
365A TYR* 4.3 3.3 - - - -
400A GLN 3.1 10.9 + - - -
401A MET 3.5 0.4 + - - -
402A LYS 3.2 0.4 - - - -
403A ARG* 1.3 77.4 - - - +
405A TYR* 1.3 59.7 + - - +
407A ARG* 3.3 6.0 + - - +
408A ILE* 3.3 28.5 + - - +
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 3.7 12.6 - - + -
368A ILE* 4.1 19.5 - - + -
387A LEU* 3.7 9.1 - - + +
401A MET* 2.8 57.6 - - + +
402A LYS 3.3 1.9 + - - +
404A GLY* 1.3 73.2 - - - +
406A GLU* 1.3 61.4 + - - +
408A ILE* 3.2 5.5 + - - +
409A TYR* 3.0 61.7 + + + -
426A LEU* 5.9 0.2 - - + -
429A PHE* 4.0 3.9 - + - -
430A VAL* 4.2 13.0 - - + -
433A CYS* 3.2 29.3 - - - +
439A ILE* 3.9 19.3 - - + -
443A LEU* 3.6 25.8 - - + -
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LYS* 3.1 47.1 + - - +
403A ARG* 3.7 14.6 - - - +
405A TYR* 1.3 77.1 - - - +
407A ARG* 1.3 60.7 + - - +
409A TYR* 3.5 7.8 + - + +
410A ASN* 3.1 25.3 + - - +
443A LEU* 4.9 4.6 - - + +
446A LEU* 3.7 31.8 - - + +
221B LYS* 4.0 13.7 + - - -
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 3.0 34.4 + - - -
362A GLU* 2.9 30.1 + - - -
365A TYR* 3.3 55.7 - - + +
403A ARG* 3.1 45.9 + - - +
404A GLY* 3.5 8.3 - - - +
405A TYR 3.2 0.2 - - - -
406A GLU* 1.3 76.8 - - - +
408A ILE* 1.3 62.4 + - - +
410A ASN* 3.2 9.2 + - - +
411A GLU* 3.2 32.0 + - - +
326B HIS* 3.1 20.5 + - + -
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 3.5 40.8 - - + +
368A ILE* 3.4 35.4 - - + -
369A ILE* 4.9 3.6 - - + +
372A LEU* 5.0 6.5 - - + -
404A GLY 3.3 20.8 + - - +
405A TYR* 3.2 8.6 + - - +
407A ARG* 1.3 78.8 - - - +
409A TYR* 1.3 75.7 + - + +
411A GLU* 3.0 4.5 + - - +
412A ILE* 2.8 35.1 + - + +
415A ILE* 4.8 4.7 - - + +
426A LEU* 3.7 28.0 - - + -
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Residues in contact with TYR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.0 43.6 + + + +
406A GLU* 3.8 9.4 - - - +
408A ILE* 1.3 80.8 - - + +
410A ASN* 1.3 59.3 + - - +
412A ILE* 3.5 19.1 - - - +
413A PRO* 3.9 4.5 - - - +
426A LEU* 3.3 34.1 - - + -
430A VAL* 2.7 33.6 - - + +
439A ILE* 4.7 0.3 - - - +
443A LEU* 3.5 28.3 + - + -
446A LEU* 3.9 16.4 - - + +
447A CYS* 3.6 15.7 - - + -
448A PRO* 3.7 22.6 - - + +
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU 3.1 13.0 + - - +
407A ARG* 3.2 14.1 - - - +
408A ILE 3.0 0.6 - - - -
409A TYR* 1.3 79.2 - - - +
411A GLU* 1.3 63.1 + - + +
412A ILE 3.5 0.2 - - - -
413A PRO* 3.5 12.5 - - - +
414A ASP* 5.9 0.7 - - - -
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 2.4 44.0 + - - -
407A ARG* 3.2 16.4 + - - +
408A ILE 3.0 2.1 + - - +
410A ASN* 1.3 82.9 - - + +
412A ILE* 1.3 61.1 + - - +
413A PRO* 3.3 3.8 - - - -
414A ASP* 2.9 16.6 + - + +
415A ILE* 2.9 42.5 + - + +
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 4.1 20.4 - - + -
408A ILE* 2.8 14.9 + - + +
409A TYR* 3.5 16.6 - - - +
411A GLU* 1.3 79.2 - - - +
413A PRO* 1.3 74.2 - - + +
415A ILE* 4.2 8.3 - - + -
416A ASN* 2.8 27.4 + - - +
422A SER* 3.7 36.1 - - - +
423A TYR* 3.7 39.7 - - + +
426A LEU* 4.3 13.9 - - + -
448A PRO* 3.8 11.9 - - + -
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Residues in contact with PRO 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A TYR 3.9 4.7 - - - +
410A ASN 3.5 14.6 - - - +
411A GLU 3.3 5.4 - - - -
412A ILE* 1.3 98.7 - - + +
414A ASP* 1.3 64.4 + - - +
416A ASN* 3.8 6.4 - - - +
417A LEU* 3.4 21.0 - - - +
423A TYR* 3.5 23.6 - - + +
448A PRO* 5.9 1.6 - - + -
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Residues in contact with ASP 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ASN 5.9 0.7 - - - -
411A GLU* 2.9 15.8 + - + +
413A PRO* 1.3 82.6 - - - +
415A ILE* 1.3 61.5 + - + +
416A ASN 3.2 1.8 - - - -
417A LEU* 2.8 38.3 + - + +
418A ASP* 3.7 8.6 + - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 5.2 2.7 - - + +
369A ILE* 5.4 11.7 - - + -
372A LEU* 4.4 24.7 - - + -
373A GLU* 6.1 1.1 - - + -
408A ILE* 4.8 7.6 - - + +
411A GLU* 2.9 41.1 + - + +
412A ILE* 4.0 10.1 - - + +
414A ASP* 1.3 74.7 - - + +
416A ASN* 1.3 55.1 + - - +
418A ASP* 2.9 6.1 + - - +
419A VAL* 2.8 47.9 + - + +
422A SER* 3.6 17.0 - - - +
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Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE 2.8 19.7 + - - +
413A PRO 3.8 6.3 - - - +
414A ASP 3.2 0.2 - - - -
415A ILE* 1.3 77.3 - - - +
417A LEU* 1.3 65.8 + - + +
418A ASP 3.2 1.2 + - - -
419A VAL 3.5 12.5 + - - +
420A PRO* 4.4 3.3 - - - +
421A HIS* 4.2 5.0 + - - -
422A SER* 3.3 30.3 + - - -
423A TYR* 3.2 38.5 + - + +
450A ARG* 4.1 17.8 - - - +
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PRO 3.4 18.6 - - - +
414A ASP* 2.8 21.2 + - - +
416A ASN* 1.3 82.0 - - + +
418A ASP* 1.3 66.0 + - - +
450A ARG* 6.0 3.6 - - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP 3.7 8.3 + - - +
415A ILE* 2.9 7.4 + - - +
417A LEU* 1.3 87.0 - - - +
419A VAL* 1.3 69.0 + - + +
420A PRO* 3.4 10.9 - - - +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 3.3 29.4 - - + +
373A GLU* 4.2 22.9 - - + +
415A ILE* 2.8 29.1 + - + +
416A ASN 3.5 6.9 - - - +
418A ASP* 1.3 83.0 - - + +
420A PRO* 1.3 71.6 - - + +
421A HIS 3.4 0.3 + - - -
422A SER* 2.5 36.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il